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NM_000489.6(ATRX):c.7439G>A (p.Arg2480Lys) AND Alpha thalassemia-X-linked intellectual disability syndrome

Germline classification:
Likely benign (2 submissions)
Last evaluated:
Aug 2, 2023
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV001279979.8

Allele description [Variation Report for NM_000489.6(ATRX):c.7439G>A (p.Arg2480Lys)]

NM_000489.6(ATRX):c.7439G>A (p.Arg2480Lys)

Gene:
ATRX:ATRX chromatin remodeler [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Xq21.1
Genomic location:
Preferred name:
NM_000489.6(ATRX):c.7439G>A (p.Arg2480Lys)
HGVS:
  • NC_000023.11:g.77508391C>T
  • NG_008838.3:g.282879G>A
  • NM_000489.6:c.7439G>AMANE SELECT
  • NM_138270.5:c.7325G>A
  • NP_000480.3:p.Arg2480Lys
  • NP_612114.2:p.Arg2442Lys
  • LRG_1153:g.282879G>A
  • NC_000023.10:g.76763869C>T
  • NM_000489.3:c.7439G>A
Protein change:
R2442K
Links:
dbSNP: rs369871569
NCBI 1000 Genomes Browser:
rs369871569
Molecular consequence:
  • NM_000489.6:c.7439G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_138270.5:c.7325G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Alpha thalassemia-X-linked intellectual disability syndrome (ATRX)
Synonyms:
ALPHA-THALASSEMIA/MENTAL RETARDATION SYNDROME, X-LINKED; ATR-X syndrome; Alpha thalassemia mental retardation syndrome, nondeletion type, X-linked; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0010519; MedGen: C1845055; Orphanet: 847; OMIM: 301040

Recent activity

Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001467120Natera, Inc.
no assertion criteria provided
Uncertain significance
(Sep 11, 2020) 		germlineclinical testing

SCV001624909Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Likely benign
(Aug 2, 2023) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Natera, Inc., SCV001467120.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001624909.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024